Several small changes and tweaks for patch release

[akohlmey]

Summary

Final set of small changes for the upcoming patch release.

Related Issues

supersedes and closes #1381

Author(s)

Axel Kohlmeyer (Temple U)

Licensing

By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).

Backward Compatibility

yes.

Implementation Notes

Individual changes are:

• change argument to git -C to be the toplevel source dir instead of the .git folder to avoid spurious modified flag in git describe.
• include PR Put #ifdef around #include "curl/curl.h" in kim_query.cpp #1381 to make KIM package compile when libcurl development package is not available
• revert order of building developer pdf and manual pdf to what it was last with htmldoc
• correct data file for micelle example to have correct periodic images for bonded atoms. add rigid body example input
• bugfix for checking image flags for consistency provided by @sjplimp

Post Submission Checklist

Please check the fields below as they are completed after the pull request has been submitted. Delete lines that don't apply

• The feature or features in this pull request is complete
• Licensing information is complete
• Corresponding author information is complete
• The source code follows the LAMMPS formatting guidelines
• The feature has been verified to work with the conventional build system
• The feature has been verified to work with the CMake based build system

[sjplimp]

in.micelle-rigid should be in.micelle.rigid for consistency,
the data.micelle file does not have image flags but just shifting some atoms outside the box?

[akohlmey]

in.micelle-rigid should be in.micelle.rigid for consistency,

done

the data.micelle file does not have image flags but just shifting some atoms outside the box?

this is in accord with the documentation. for PBC those are created after reading. only with fixed boundaries, the atoms outside the box would be discarded.